A Meta-Analysis Reveals Opposite Effects of Biotic and Abiotic Stresses on Transcript Levels of Arabidopsis Intracellular Immune Receptor Genes

Abstract

Plant intracellular immune receptor NLR (nucleotide-binding leucine-rich repeat) proteins sense the presence of pathogens and trigger strong and robust immune responses. NLR genes are known to be tightly controlled at the protein level, but little is known about their dynamics at the transcript level. In this study, we presented a meta-analysis of transcript dynamics of all 207 NLR genes in the Col-0 accession of Arabidopsis thaliana under various biotic and abiotic stresses based on 88 publicly available RNA sequencing datasets from 27 independent studies. We find that about two thirds of the NLR genes are generally induced by pathogens, immune elicitors, or salicylic acid (SA), suggesting that transcriptional induction of NLR genes might be an important mechanism in plant immunity regulation. By contrast, NLR genes induced by biotic stresses are often repressed by abscisic acid, high temperature and drought, suggesting that transcriptional regulation of NLR genes might be important for interaction between abiotic and biotic stress responses. In addition, pathogen-induced expression of some NLR genes are dependent on SA induction. Interestingly, a small group of NLR genes are repressed under certain biotic stress treatments, suggesting an unconventional function of this group of NLRs. This meta-analysis thus reveals the transcript dynamics of NLR genes under biotic and abiotic stress conditions and suggests a contribution of NLR transcript regulation to plant immunity as well as interactions between abiotic and biotic stress responses.

Keywords: Arabidopsis; NLR; abiotic stress; biotic stress; intracellular immune receptor.

Figure 1

Transcript dynamics of NLR genes during biotic and abiotic stresses. (A–J) Line graphs showing the number of induced (red color) and repressed (blue color) NLR genes at each time point for different treatments. The numbers are made based on Table 1. For biotic stress treatments, the maximum number of induced NLR genes and the total DEG number are listed as induced NLR number/total DEG number above the corresponding time point. Similarly for abiotic stress treatments, the maximum number of repressed NLR genes and the corresponding total DEGs are listed. “h” indicates “hours” and “d” means “days”.

Figure 2

Expression profile of 178 NLR genes as well as 17 SA- and NHP-related genes under stress conditions and in autoimmune mutants. Cluster display of 178 NLR or NLR-like genes along with 17 SA- and NHP-related genes by their transcript levels in 37 conditions. Gene induction is marked as a red box while gene repression is marked as a blue box. Expression not altered are left as blank. Modules A, B, C, and D are discussed in the text. The detailed information of the genes from each module is shown in the right tables, including gene ID number on TAIR website, common name, NLR type, and whether genes are experimentally validated or not. In the tables, 17 SA- and NHP-related genes are colored red. “EV-NLR” means “experimentally validated NLRs” defined by Kourelis and Kamoun (2020). The letter on the left of a gene indicates that this gene is co-regulated with at least another gene in the respective gene cluster and the same letter before the gene ID indicates genes are in the same gene cluster on the chromosome. The 37 conditions are numbered and they are (1) 4°C, 24 h; (2) 4°C, 24 h; (3) 10°C, 1 h; (4) 10°C, 24 h; (5) 35°C, 4 h; (6) 37°C, 3 h; (7) 37°C, 6 h; (8) 44°C, 1 h; (9) ABA, 3 h, 50 μM; (10) ABA, 6 h, 100 μM; (11) ABA, 60 h, 10 μM; (12) ABA, 3 h, 50 μM; (13) drought, 7 days; (14) NaCl, 1 h, 150 mM; (15) NaCl, 24 h, 150 mM; (16) low water potential, −0.7 Mpa, 96 h; (17) Pst DC3000, 24 hpi, OD₆₀₀ of 0.001; (18) Pst DC3000, 12 hpi, 107 cfu/ml; (19) Pst DC3000, 24 hpi, OD₆₀₀ of 0.2; (20) Pst DC3000 AvrRpt2, 4 hpi, infiltration, OD₆₀₀ of 0.001; (21) Pst DC3000 AvrRps4, 6 hpi, 107 cfu/ml; (22) Pst DC3000 AvrRpm1, 24 hpi, OD₆₀₀ of 0.001; (23) Pst DC3000 AvrRpm1, 3 day, 10 h after dawn, OD₆₀₀ of 0.02; (24) Pst DC3000 cor-, 24 hpi, OD₆₀₀ of 0.2; (25) B. cinerea B05.10, 24 hpi, 5 μl 1 ×10⁵ spores/ml; (26) B. cinerea 2100, 14 hpi, 2 μl 2.5 ×10⁵ spores/ml; (27) flg22, 30 min, 100 nM; (28) flg22, 30 min, 1 μM; (29) flg22, 1 h, 1 μM; (30) chitin, 3 h, 40 mM; (31) SA, 1 h, 50 μM; (32) BTH, 5 h, spray, 300 μM; (33) acd6-1, ZT13, 1 h after darkness onset; (34) acd6-1, ZT1, 1 h after light onset; (35) bak1-4 serk4-1; (36) ssi2-1; (37) hos15-4/smo1. References and detailed information for these conditions (1–37) are in Supplementary Data 1. Abiotic stresses are colored gray, biotic stresses are colored magenta, and autoimmune mutants are colored orange. “h” indicates “hour” and “hpi” means “hour(s) post inoculation”.

Figure 3

Expression profile of 207 NLR genes as well as 17 SA- and NHP-related genes under time-course biotic stress treatment. Expression levels of 207 NLR or NLR-like genes and 17 SA- and NHP-related genes during the time course of biotic stress treatments that are marked as triangles (light gray for Pst DC3000; dark gray for avirulent pathogens including Pst DC3000 AvrRpt2, Pst DC3000 AvrRpm1, and Pst DC3000 AvrRps4; light blue for B. cinerea; orange for flg22; and yellow for BTH). The genes are ordered by their induction by SA and BTH (first ordered by the induction by SA, then ordered by the induction by BTH), from induced (indicated by red square), to non-alteration (blank) and repressed (blue square) from top to bottom. These genes are grouped into I (dark red), II (orange), III (gray), and IV (dark blue) four groups based on the transcript changes under biotic stresses as discussed in Results. NLR genes that exhibited a reduced expression or an increased expression in the cbp60g sard1 mutant compared to the wild type at 24 hpi after P. syringae pv maculicola ES4326 infection are displayed as blue square or red square, respectively, in the last column of the expression heatmap. The 17 SA- and NHP-related genes are colored red. The 15 NLR genes dependent on SA and the 8 NLR genes of which full induction is dependent on SA are highlighted with yellow and light blue, respectively. The detailed information of the genes from each group is shown in the right tables, including gene ID number on TAIR website, common name, NLR type, and whether genes are upregulated (up) or downregulated (down) in the cbp60g sard1 mutant compared to wild-type plant at 24 hpi after P. syringae pv maculicola ES4326 infection.

Figure 4

Number of NLR genes with altered expression in the cbp60g sard1 double mutant. (A) Number of NLR DEGs in each group in the cbp60g sard1 mutant and the wild type in response to P. syringae pv maculicola ES4326. DEGs were extracted from GSE10087 (Lu et al., 2018) by in-house pipeline with p < 0.05. “Up” and “Down” indicate increased or reduced expression in the mutant compared to the wild type, respectively. (B) Venn diagrams showing SA-dependent NLR gene induction by pathogen. The left panel is NLR genes induced by Pma in wild type and NLR genes in the cbp60g sard1 double mutant. The middle panel is the NLR genes induced by Pma only in wild type and NLR genes upregulated in cbp60g sard1 double mutant compared to the wild type under mock induction. The right panel shows the NLR genes induced by Pma in wild type and NLR genes downregulated in cbp60g sard1 double mutant compared to wild type after Pma infection. The number of NLR genes whose pathogen induction or whose full induction are dependent on CBP60G/SARD1 is highlighted with yellow. Pma, P. syringae pv maculicola ES4326.